BIO 12.
01 NOTES o Guanine (G) – 3 hydrogen bonds – Cytosine
Central Dogma of Life
- A rule that all organisms go by
- Flow of biological information
- Concerned with producing proteins
REPLICATION
- DNA double helix is separated (unwound) and
then duplicated, producing two double helices
- Expose the nitrogenous bases allowing for a
new connection
- Resulting in 4 strands
Universal Features of Replication
- Semi-conservative manner
o 2 resulting double helices consist of 1
progeny and 1 parental strand
- Specific base pairing
o Adenine (A) – 2 hydrogen bonds – Thymine
(T)
(C)
- Bidirectional
o form the origin of replication, replication
forks are formed
-
D
irection of Synthesis: 5’ -> 3’ (new strand)
o DNA polymerase synthesizes new strand
only at the 3’ end
o Template must be a 3’ -> 5’ strand for
replication to be continuous
o Attachment of new nucleotide is always at
the free 3’-OH end
o Since DNA polymerase cannot start new
chains, primers are sites wherein the DNA
polymerase can bind and begin DNA
synthesis
o Primase – enzymes of RNA primer
REPLICATION PROCESS
INITIATION
- The DNA helix must be opened up (now called
DNA helices)
- “-ase” – suffix indicating enzyme
- DNA helix is now unwound making the
nitrogenous bases exposed
- Helicase (the unzipping enzyme) – breaks up
the hydrogen bonds holding the bases together
opening up the DNA strand and exposing the
bases
o Results in the formation of a replication
fork
- Single-strand binding protein – stabilize the
unwound strands and prevents the reattachment
of the bases
- Origin of replication (DNA helix) – the
starting point of replication
- Primase – starts the process by making small
pieces of RNA primers (allows the DNA
polymerase a place to begin)
- DNA polymerase – binds to the primer and will
make the new strand of DNA
o Can only add DNA bases in one direction
(5’end -> 3’end)
o Cannot add nucleotides or start DNA
replication without the primase that adds the
RNA primer
ELONGATION
- Begins with the attachment of DNA
polymerase III
o Adds nucleotide units
o Works off of what the RNA primase started
(attached RNA primers)
- Leading Strand – made continuously
o Created from the 5’ -> 3’ direction
o Replication here occurs TOWARDS the
replication fork (paths that have
separated/where helicase is)
- DNA polymerase III will continue to elongate
as long as the helicase opens up new segments
of the DNA
o It will continue synthesizing and adding new
nucleotide units to the 3’ -> 5’ strand as long
as the helicase opens up
- Lagging Strand – cannot be made in a
continuous direction because it runs in the
opposite direction (opposite of the leading
strand)
o the DNA polymerase can therefore only
make this strand in a series of small chunks
called Okazaki Fragments (short fragments
of DNA created in the lagging strand)
o Each fragment is started with an RNA
primer (by the primase)
o It starts adding the primer at the bottom
where the helicase is (always where the
helicase is because it indicates where the
point of replication is)
o DNA polymerase then adds a short row of
DNA bases in a 5’ to 3’ direction
o This time, replication occurs AWAY from
the replication fork
o DNA polymerase I – attach then remove
RNA primers and replace it with DNA – it
needs to remove those primer because those
are RNA, and what’s being made is DNA
(exonuclease)
o DNA ligase/s – act as a glue and seal the
spaces (gap) that are present in the DNA
strand (may seal by putting N-bases)
 This is more obvious in lagging strand
 Moves through the DNA strand and
looks for spaces and then seals it
 Once the ligases seal, other enzymes
present will now disassociate
SHORT SUMMARY
Lagging Strand
- A new primase enters, adds RNA primers
allowing DNA polymerase III to synthesize and
elongate the strand
- Replication occurs away from the replication
fork
Leading Strand
- Replication occurs towards the replication fork,
adding new nucleotides will be easier because
there is always a 3’-OH
- Not so much problem because it continuously
creates new DNA strand
TERMINATION
POSSIBILITIES:
- Genetically-determined sites – somewhere along
the DNA sites allows for replication to occur
(possible due to POTEEN-TUS binding in the
terminal region called Ter sites)
o Secondary structure hiders the replication
fork
o Protein (Tus) binds the terminal region (Ter
sites), blocking the progress of the
replication forks
- Replication forks converging (particularly in
prokaryotes)
- Synthesis completion – the cell has now
fulfilled its job (no need for replication
anymore)
REPLICATION PROCESS REVIEW
- Continuous replication (3’ -> 5’) template
strand for continuous DNA replication because
of the antiparallel feature
- 5’ -> 3’ – lagging strand may be found
- Helicase – the first one to open up the DNA
strand
- Single strand binding proteins (SSBPs) –
stabilize and prevents the reattachment of the
unwound strands
- RNA primers – facilitated by the RNA primases
(initiate the DNA synthesis/replication)
- Always add the primer where the helicase is
TRANSCRIPTION
- mRNA derived from the DNA is used to
produce proteins
- it is then transcribed into mRNA (or messenger
RNA)
- the DNA template that was replicated is going
to serve as the pattern to create mRNA
- serves as the in-between of DNA and protein
- the genetic code is in DNA but it is in a
language the cell cannot understand yet which
has to be transcribed into mRNA which will
eventually be translated into proteins
- Differences tie in their chemical structure,
particularly in carbon 2 (RNA – OH : DNA – H)
more unstable due to allowing other chemical
attachments
- Complimentary RNA – Uracil (U) instead of
Thymine (T)
- In eukaryotes, the first 2 processes (replication
& transcription) will both occur in the nucleus
(nucleoid region). However, the translation
process occurs outside (this differs in
prokaryotic organisms as they do not possess
any membrane-bound organelle)
- Ribosomes are closest to the nucleus, something
like an extension
- Product of transcription (mRNA, RNA) usually
transported to the nucleus to be processed into
proteins
FEATURES OF TRANSCRIPTION
- DNA is used as a template to create mRNA
- mRNA synthesis proceeds from a 5’ -> 3’
direction
o similar for replication (direction of
synthesis)
o template (DNA) should be 3’ -> 5’
- Primary enzyme - RNA polymerase
o Can initiate new strands
o No primers needed
Biological Flow of Information
- Replication – DNA is used as a template to
create
- Transcription – mRNA is used as a template to DNA (where the promoter region is) signaling
create the start of the transcription process
- Translation – proteins o Only ONE (1) of the two strands of the
DNA will be transcribed into mRNA (since
RNA POLYMERASE RNA is single-stranded)
o Direction of synthesis in RNA is 5’ -> 3’
(same in DNA)

ELONGATION

- can start and initiate new strands on its own (no

need for primer unlike in DNA polymerase)
- a complex of different subunits/enzymes that
simply refers to the RNA polymerase core
enzyme
- 5 subunits making up the enzyme:
o β, β’, 2 α, ω (omega), σ(sigma)
o Omega factor for assembling all subunits (a
- When the RNA core enzyme + sigma factor has
glue that holds all subunits and other
traveled a bit down the DNA template and
factors) together
created the short stretch of RNA:
 Allows connection to make up the RNA
o Sigma factor will then disassociate (since it
core enzyme
already helped the core enzyme recognize
o Sigma factor for site recognition (area where
the promoter region)
transcription will take place) or the area
o Left behind is the RNA polymerase core
where transcription begin
which will continue traveling down the
 Can also disassociate
DNA template in which the RNA strand will
 Promoter region – specific region
become longer (as it is being transcribed)
where transcription will initiate, series of
- Transcription Bubbles – small opening and
nitrogenous bases, where sigma factor
forms as soon as the core enzyme travels down
will bind and begin transcribing the
(temporary and closes down again)
mRNA (in DNA replication, it is the
origin of replication)

TRANSCRIPTION PROCESS
RECOGNITION

- Sigma factor + core enzyme (RNA polymerase)

will come together and will bind to the strand of
- mRNA strand is the same as the coding strand,
TRANSLATION
except thymine (T) as this will now become
- mRNA used as template to produce proteins
uracil (U)
- basis on the genetic code; read in groups of
TERMINATION three (3) called CODONS (triplet bases –
nitrogenous bases group into 3)
- where proteins are produced using mRNA

- usually happens when the RNA polymerase

where it encounters a GC rich segment of the
DNA
o GC (Guanine + Cytosine) pairing because of
the 3 hydrogen bonds - proteins = polypeptides/amino acids
o Terminates/reverts back to its original state - proteins are now in a language that cell
understands
o G=C rich pairing will then reattach (because
- Catalytic proteins (enzymes) – facilitate
of the bond)
metabolic reactions and processes
- RNA polymerase will then disassociate, leaving
- Structural proteins (cell integrity) – found in
behind the mRNA strand and the DNA template
cell membrane, cell wall, etc.; for cell integrity
strand + complementary strand alone
- Building blocks of proteins are call AMINO
- Termination is completed once the mRNA
ACIDS
strands form a stem-loop structure (like a knot at
- Then connected amino acids are then the
the end)
proteins!
o Bookmarking the end of the process

STRUCTURE OF AMINO ACIDS

- Central Carbon – also called as alpha carbon,
central to all other chemical structures
- Carboxylic acid group (-COOH) – indicated as
the C-O-OH
- Amino group (-NH2) – H2N
- R-group (side chains of AA) – can be think of
as a variable (making the others as constants)
o Indicate amino acids - To create protein, must have several amino
o R-groups are different acids in a chain
- Dipeptide – when there are 2 amino acids - Dehydration synthesis/process – to create (or
- Tripeptides – when there are 3 amino acids the process of removing water
- Polypeptides/protein – when there are 4 or H2ON/dehydration)
more amino acids

How AMINO ACIDS connects to each other:

- N-terminus – ends of amino acids (terminal

nitrogen)
- G-terminus – indicated by the last carbon (last
C)
GENETIC CODE
- CODONS
o Protein = language; Codons = words
o Triplet bases
o Does not always happen that you divide
codons at the beginning, it may be in the
middle of the sequence of even at the end.
- Codon Table:

PROPERTIES OF THE GENETIC CODE

- 22 amino acids, 64 codons
- Codon at a specific site identifies the AA (or
amino acids)
- Degenerate code – there is no one-to-one
correspondence between code and ‘word’
- Each
amino
acid
may

correspond to several codons